The nonhistone chromosomal (NHC) proteins of rat liver chromatin possess the properties required of specific DNA binding probes in rat liver chromosomes. We have isolated a class of NHC-proteins which have a preference for its homologous DNA over other eukaryotic DNAs. The objective of this research is to characterize the heterogeneity of the class of NHC-proteins by use of polyacrylamide dis gel electrophoresis and to determine the complexity of the DNA binding sites by DNA reassociation techniques. The DNA protein interactions can be investigated by determining the conditions of optimum specificity by the use of the retention properties of protein-DNA complexes on membrane filters and characterizing the chemical interactions between the protein probes and the DNA binding sites by fluorescence and circular dichroism techniques. With the chemical characteristics defined, the distribution of the binding sites with respect to the sequence distribution of repetitive sequences of the rat genome can be determined.